Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr3c1

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
liver
strain
C57BL/6J
treatment
CLP operation followed after 06h by injection of PBS (IP) with organ isolation 2h later
chip antibody
Anti-GR (H300, sc-8992; Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
50mg of tissue was homogenized in PBS and then crosslinked with 2% formaldehyde in PBS for 20 min at RT while rotating. This reaction was stopped by adding 125mM glycine for 10min at RT. Tissue was then collected in ice-cold PBS and subsequently lysed in lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM Tris pH8, supplemented with protease inhibitors). Lysates were sonicated at 4°C to yield 200-800bp DNA fragments. IP was performed on 100µl lysates diluted 1:3 in incubation buffer (0.15% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA and 20mM HEPES) with 5µg of rabbit anti-GR antibody (H300, sc-8992; Santa Cruz) fter two hours BSA blocked nProtein sepharose beads (GE Healthcare) were added to the lysates. The following day, beads were washed in WBI, WBII, LiCl buffer and twice in EDTA/HEPES buffer (0.5M EDTA and 1M HEPES). Chromatin was eluted in 200µl elution buffer (0,1M NaHCO3 and 10% SDS) supplemented with proteinase K. Next, proteins were decrosslinked by raising the incubation temperature to 65°C for 16h and DNA purified using the PCR purification kit (Qiagen), and eluting in 50µl of Qiagen Elution Buffer TruSeq ChIP Library Preparation Kit

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

mm10

Number of total reads
21252388
Reads aligned (%)
97.7
Duplicates removed (%)
8.7
Number of peaks
1045 (qval < 1E-05)

mm9

Number of total reads
21252388
Reads aligned (%)
97.5
Duplicates removed (%)
8.8
Number of peaks
1033 (qval < 1E-05)

Base call quality data from DBCLS SRA